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Contents |
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115 a.a.
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123 a.a.
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173 a.a.
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* Residue conservation analysis
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PDB id:
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DNA binding protein
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Title:
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Structure of the human replication protein a (rpa) trimerization core
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Structure:
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Replication protein a 14 kda subunit. Chain: a, d. Fragment: rpa14. Engineered: yes. Replication protein a 32 kda subunit. Chain: b, e. Fragment: rpa32 central domain (residues 44-171). Engineered: yes. Replication protein a 70 kda DNA-binding subunit.
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Gene: rfa3_human. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: rfa2_human. Gene: rfa1_human.
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Biol. unit:
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Hexamer (from
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Resolution:
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2.80Å
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R-factor:
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0.236
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R-free:
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0.282
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Authors:
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E.V.Bochkareva,S.Korolev,S.P.Lees-Miller,A.Bochkarev
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Key ref:
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E.Bochkareva
et al.
(2002).
Structure of the RPA trimerization core and its role in the multistep DNA-binding mechanism of RPA.
EMBO J,
21,
1855-1863.
PubMed id:
DOI:
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Date:
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19-Feb-02
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Release date:
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05-Jun-02
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PROCHECK
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Headers
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References
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P35244
(RFA3_HUMAN) -
Replication protein A 14 kDa subunit from Homo sapiens
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Seq:
Struc:
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121 a.a.
115 a.a.
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Enzyme class:
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Chains A, B, C, D, E, F:
E.C.?
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DOI no:
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EMBO J
21:1855-1863
(2002)
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PubMed id:
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Structure of the RPA trimerization core and its role in the multistep DNA-binding mechanism of RPA.
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E.Bochkareva,
S.Korolev,
S.P.Lees-Miller,
A.Bochkarev.
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ABSTRACT
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The human single-stranded DNA-binding protein, replication protein A (RPA) binds
and stable
( approximately 30 nt). Switching from 8 to 30 nt mode is associated with a
large conformational change. Here we report the 2.8 A structure of the RPA
trimerization core comprising the C-terminal DNA-binding domain of subunit RPA70
(DBD-C), the central DNA-binding domain of subunit RPA32 (DBD-D) and the entire
RPA14 subunit. All three domains are built around a central
oligonucleotide/oligosaccharide binding (OB)-fold and flanked by a helix at the
C-terminus. Trimerization is mediated by three C-terminal helices arranged in
parallel. The OB-fold of DBD-C possesses unique structural features; embedded
zinc ribbon and helix-turn-helix motifs. Using time-resolved proteolysis with
trypsin, we demonstrate that the trimerization core does not contribute to the
binding with substrates of 10 nt, but interacts with oligonucleotides of 24 nt.
Taken together, our data indicate that switching from 8-10 to 30 nt mode is
mediated by DNA binding with the trimerization core.
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Selected figure(s)
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Figure 3.
Figure 3 DBD-C modeled on a ssDNA molecule derived from the
DBD-AB/ssDNA co-crystal structure. The DBD-C was aligned with
DBD-B as shown in Figure 2C and then docked onto the 3 nt DBD-B
binding site (shown in red). Side chains in DBD-C (the position
for Y581 is putative) that are orientated to interact with the
sugar-phosphate backbone are colored in green and blue (for
carbon and nitrogen atoms, respectively), and those in position
to hydrogen bond, or stack with, DNA bases are yellow. Putative
hydrogen bonds with the phosphate groups are shown as dashed
lines. The position of conserved C486 is shown as a reference.
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Figure 6.
Figure 6 Suggested model of the apo RPA trimer. Cartoon
representing RPA as a hexamer of OB-folds centered around a
multi-helical bundle. Helices are represented by circles, and
the six OB-folds by palms, which are labeled as 14, 70-NTD
(N-terminal domain), A, B, C and D (for RPA14, RPA70N, DBD-A,
-B, -C and -D, respectively). The trimerization core is outlined
with a triangle. Putative elements, an interaction between
RPA70N and RPA14, and the transient helix of RPA70N, are shown
with question mark. See text for more details.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2002,
21,
1855-1863)
copyright 2002.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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J.G.Glanzer,
S.Liu,
and
G.G.Oakley
(2011).
Small molecule inhibitor of the RPA70 N-terminal protein interaction domain discovered using in silico and in vitro methods.
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Bioorg Med Chem,
19,
2589-2595.
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J.Sun,
Y.Yang,
K.Wan,
N.Mao,
T.Y.Yu,
Y.C.Lin,
D.C.Dezwaan,
B.C.Freeman,
J.J.Lin,
N.F.Lue,
and
M.Lei
(2011).
Structural bases of dimerization of yeast telomere protein Cdc13 and its interaction with the catalytic subunit of DNA polymerase α.
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Cell Res,
21,
258-274.
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PDB codes:
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M.Wu,
Y.J.Park,
E.Pardon,
S.Turley,
A.Hayhurst,
J.Deng,
J.Steyaert,
and
W.G.Hol
(2011).
Structures of a key interaction protein from the Trypanosoma brucei editosome in complex with single domain antibodies.
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J Struct Biol,
174,
124-136.
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PDB codes:
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D.I.Pretto,
S.Tsutakawa,
C.A.Brosey,
A.Castillo,
M.E.Chagot,
J.A.Smith,
J.A.Tainer,
and
W.J.Chazin
(2010).
Structural dynamics and single-stranded DNA binding activity of the three N-terminal domains of the large subunit of replication protein A from small angle X-ray scattering.
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Biochemistry,
49,
2880-2889.
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F.Wang,
Y.Yang,
T.R.Singh,
V.Busygina,
R.Guo,
K.Wan,
W.Wang,
P.Sung,
A.R.Meetei,
and
M.Lei
(2010).
Crystal structures of RMI1 and RMI2, two OB-fold regulatory subunits of the BLM complex.
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Structure,
18,
1159-1170.
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PDB codes:
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I.De Vlaminck,
I.Vidic,
M.T.van Loenhout,
R.Kanaar,
J.H.Lebbink,
and
C.Dekker
(2010).
Torsional regulation of hRPA-induced unwinding of double-stranded DNA.
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Nucleic Acids Res,
38,
4133-4142.
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K.A.Hoadley,
D.Xu,
Y.Xue,
K.A.Satyshur,
W.Wang,
and
J.L.Keck
(2010).
Structure and cellular roles of the RMI core complex from the bloom syndrome dissolvasome.
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Structure,
18,
1149-1158.
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PDB code:
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M.J.Giraud-Panis,
M.T.Teixeira,
V.Géli,
and
E.Gilson
(2010).
CST meets shelterin to keep telomeres in check.
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Mol Cell,
39,
665-676.
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M.Paschini,
E.K.Mandell,
and
V.Lundblad
(2010).
Structure prediction-driven genetics in Saccharomyces cerevisiae identifies an interface between the t-RPA proteins Stn1 and Ten1.
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Genetics,
185,
11-21.
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R.L.Flynn,
and
L.Zou
(2010).
Oligonucleotide/oligosaccharide-binding fold proteins: a growing family of genome guardians.
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Crit Rev Biochem Mol Biol,
45,
266-275.
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S.J.Haring,
T.D.Humphreys,
and
M.S.Wold
(2010).
A naturally occurring human RPA subunit homolog does not support DNA replication or cell-cycle progression.
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Nucleic Acids Res,
38,
846-858.
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S.S.Krishna,
L.Aravind,
C.Bakolitsa,
J.Caruthers,
D.Carlton,
M.D.Miller,
P.Abdubek,
T.Astakhova,
H.L.Axelrod,
H.J.Chiu,
T.Clayton,
M.C.Deller,
L.Duan,
J.Feuerhelm,
J.C.Grant,
G.W.Han,
L.Jaroszewski,
K.K.Jin,
H.E.Klock,
M.W.Knuth,
A.Kumar,
D.Marciano,
D.McMullan,
A.T.Morse,
E.Nigoghossian,
L.Okach,
R.Reyes,
C.L.Rife,
H.van den Bedem,
D.Weekes,
Q.Xu,
K.O.Hodgson,
J.Wooley,
M.A.Elsliger,
A.M.Deacon,
A.Godzik,
S.A.Lesley,
and
I.A.Wilson
(2010).
The structure of SSO2064, the first representative of Pfam family PF01796, reveals a novel two-domain zinc-ribbon OB-fold architecture with a potential acyl-CoA-binding role.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
66,
1160-1166.
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PDB code:
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Y.S.Krasikova,
N.I.Rechkunova,
E.A.Maltseva,
I.O.Petruseva,
and
O.I.Lavrik
(2010).
Localization of xeroderma pigmentosum group A protein and replication protein A on damaged DNA in nucleotide excision repair.
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Nucleic Acids Res,
38,
8083-8094.
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A.C.Mason,
S.J.Haring,
J.M.Pryor,
C.A.Staloch,
T.F.Gan,
and
M.S.Wold
(2009).
An alternative form of replication protein a prevents viral replication in vitro.
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J Biol Chem,
284,
5324-5331.
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A.M.Dickson,
Y.Krasikova,
P.Pestryakov,
O.Lavrik,
and
M.S.Wold
(2009).
Essential functions of the 32 kDa subunit of yeast replication protein A.
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Nucleic Acids Res,
37,
2313-2326.
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D.E.Casteel,
S.Zhuang,
Y.Zeng,
F.W.Perrino,
G.R.Boss,
M.Goulian,
and
R.B.Pilz
(2009).
A DNA Polymerase-{alpha}{middle dot}Primase Cofactor with Homology to Replication Protein A-32 Regulates DNA Replication in Mammalian Cells.
|
| |
J Biol Chem,
284,
5807-5818.
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J.Milosevic,
S.C.Schwarz,
V.Ogunlade,
A.K.Meyer,
A.Storch,
and
J.Schwarz
(2009).
Emerging role of LRRK2 in human neural progenitor cell cycle progression, survival and differentiation.
|
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Mol Neurodegener,
4,
25.
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T.R.Salas,
I.Petruseva,
O.Lavrik,
and
C.Saintomé
(2009).
Evidence for direct contact between the RPA3 subunit of the human replication protein A and single-stranded DNA.
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Nucleic Acids Res,
37,
38-46.
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W.Ma,
V.Panduri,
J.F.Sterling,
B.Van Houten,
D.A.Gordenin,
and
M.A.Resnick
(2009).
The transition of closely opposed lesions to double-strand breaks during long-patch base excision repair is prevented by the coordinated action of DNA polymerase delta and Rad27/Fen1.
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Mol Cell Biol,
29,
1212-1221.
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B.K.Benson,
G.Meades,
A.Grove,
and
G.L.Waldrop
(2008).
DNA inhibits catalysis by the carboxyltransferase subunit of acetyl-CoA carboxylase: implications for active site communication.
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Protein Sci,
17,
34-42.
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I.O.Petruseva,
I.S.Tikhanovich,
B.P.Chelobanov,
and
O.I.Lavrik
(2008).
RPA repair recognition of DNA containing pyrimidines bearing bulky adducts.
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J Mol Recognit,
21,
154-162.
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J.A.Stewart,
A.S.Miller,
J.L.Campbell,
and
R.A.Bambara
(2008).
Dynamic Removal of Replication Protein A by Dna2 Facilitates Primer Cleavage during Okazaki Fragment Processing in Saccharomyces cerevisiae.
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J Biol Chem,
283,
31356-31365.
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J.D.Bartos,
L.J.Willmott,
S.K.Binz,
M.S.Wold,
and
R.A.Bambara
(2008).
Catalysis of strand annealing by replication protein a derives from its strand melting properties.
|
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J Biol Chem,
283,
21758-21768.
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J.Tomida,
Y.Masuda,
H.Hiroaki,
T.Ishikawa,
I.Song,
T.Tsurimoto,
S.Tateishi,
T.Shiomi,
Y.Kamei,
J.Kim,
K.Kamiya,
C.Vaziri,
H.Ohmori,
and
T.Todo
(2008).
DNA damage-induced ubiquitylation of RFC2 subunit of replication factor C complex.
|
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J Biol Chem,
283,
9071-9079.
|
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P.D.Robertson,
E.M.Warren,
H.Zhang,
D.B.Friedman,
J.W.Lary,
J.L.Cole,
A.V.Tutter,
J.C.Walter,
E.Fanning,
and
B.F.Eichman
(2008).
Domain architecture and biochemical characterization of vertebrate mcm10.
|
| |
J Biol Chem,
283,
3338-3348.
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|
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S.K.Binz,
and
M.S.Wold
(2008).
Regulatory functions of the N-terminal domain of the 70-kDa subunit of replication protein A (RPA).
|
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J Biol Chem,
283,
21559-21570.
|
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|
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L.Cai,
M.Roginskaya,
Y.Qu,
Z.Yang,
Y.Xu,
and
Y.Zou
(2007).
Structural characterization of human RPA sequential binding to single-stranded DNA using ssDNA as a molecular ruler.
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Biochemistry,
46,
8226-8233.
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L.Men,
M.Roginskaya,
Y.Zou,
and
Y.Wang
(2007).
Redox-dependent formation of disulfide bonds in human replication protein A.
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Rapid Commun Mass Spectrom,
21,
2743-2749.
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P.E.Pestryakov,
Y.S.Krasikova,
I.O.Petruseva,
S.N.Khodyreva,
and
O.I.Lavrik
(2007).
The role of p14 subunit of replication protein A in binding to single-stranded DNA.
|
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Dokl Biochem Biophys,
412,
4-7.
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P.Taneja,
I.Boche,
H.Hartmann,
H.P.Nasheuer,
F.Grosse,
E.Fanning,
and
K.Weisshart
(2007).
Different activities of the largest subunit of replication protein A cooperate during SV40 DNA replication.
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FEBS Lett,
581,
3973-3978.
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R.W.Anantha,
V.M.Vassin,
and
J.A.Borowiec
(2007).
Sequential and synergistic modification of human RPA stimulates chromosomal DNA repair.
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J Biol Chem,
282,
35910-35923.
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S.J.Haring,
and
M.S.Wold
(2007).
A common means to an end.
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Nat Struct Mol Biol,
14,
176-177.
|
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V.Martín,
L.L.Du,
S.Rozenzhak,
and
P.Russell
(2007).
Protection of telomeres by a conserved Stn1-Ten1 complex.
|
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Proc Natl Acad Sci U S A,
104,
14038-14043.
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|
|
|
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E.Fanning,
V.Klimovich,
and
A.R.Nager
(2006).
A dynamic model for replication protein A (RPA) function in DNA processing pathways.
|
| |
Nucleic Acids Res,
34,
4126-4137.
|
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|
|
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|
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J.Fan,
Y.Matsumoto,
and
D.M.Wilson
(2006).
Nucleotide sequence and DNA secondary structure, as well as replication protein A, modulate the single-stranded abasic endonuclease activity of APE1.
|
| |
J Biol Chem,
281,
3889-3898.
|
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J.Majka,
S.K.Binz,
M.S.Wold,
and
P.M.Burgers
(2006).
Replication protein A directs loading of the DNA damage checkpoint clamp to 5'-DNA junctions.
|
| |
J Biol Chem,
281,
27855-27861.
|
|
|
|
|
|
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S.Kumaran,
A.G.Kozlov,
and
T.M.Lohman
(2006).
Saccharomyces cerevisiae replication protein A binds to single-stranded DNA in multiple salt-dependent modes.
|
| |
Biochemistry,
45,
11958-11973.
|
|
|
|
|
|
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X.Jiang,
V.Klimovich,
A.I.Arunkumar,
E.B.Hysinger,
Y.Wang,
R.D.Ott,
G.D.Guler,
B.Weiner,
W.J.Chazin,
and
E.Fanning
(2006).
Structural mechanism of RPA loading on DNA during activation of a simple pre-replication complex.
|
| |
EMBO J,
25,
5516-5526.
|
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|
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Y.Zou,
Y.Liu,
X.Wu,
and
S.M.Shell
(2006).
Functions of human replication protein A (RPA): from DNA replication to DNA damage and stress responses.
|
| |
J Cell Physiol,
208,
267-273.
|
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|
|
|
|
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I.Leiros,
J.Timmins,
D.R.Hall,
and
S.McSweeney
(2005).
Crystal structure and DNA-binding analysis of RecO from Deinococcus radiodurans.
|
| |
EMBO J,
24,
906-918.
|
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PDB code:
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K.M.Doherty,
J.A.Sommers,
M.D.Gray,
J.W.Lee,
C.von Kobbe,
N.H.Thoma,
R.P.Kureekattil,
M.K.Kenny,
and
R.M.Brosh
(2005).
Physical and functional mapping of the replication protein a interaction domain of the werner and bloom syndrome helicases.
|
| |
J Biol Chem,
280,
29494-29505.
|
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|
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S.D.Rider,
X.Cai,
W.J.Sullivan,
A.T.Smith,
J.Radke,
M.White,
and
G.Zhu
(2005).
The protozoan parasite Cryptosporidium parvum possesses two functionally and evolutionarily divergent replication protein A large subunits.
|
| |
J Biol Chem,
280,
31460-31469.
|
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S.M.Shell,
S.Hess,
M.Kvaratskhelia,
and
Y.Zou
(2005).
Mass spectrometric identification of lysines involved in the interaction of human replication protein a with single-stranded DNA.
|
| |
Biochemistry,
44,
971-978.
|
|
|
|
|
|
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V.U.Bai,
E.Cifuentes,
M.Menon,
E.R.Barrack,
and
G.P.Reddy
(2005).
Androgen receptor regulates Cdc6 in synchronized LNCaP cells progressing from G1 to S phase.
|
| |
J Cell Physiol,
204,
381-387.
|
|
|
|
|
|
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X.Wu,
S.M.Shell,
and
Y.Zou
(2005).
Interaction and colocalization of Rad9/Rad1/Hus1 checkpoint complex with replication protein A in human cells.
|
| |
Oncogene,
24,
4728-4735.
|
|
|
|
|
|
|
Y.Liu,
M.Kvaratskhelia,
S.Hess,
Y.Qu,
and
Y.Zou
(2005).
Modulation of replication protein A function by its hyperphosphorylation-induced conformational change involving DNA binding domain B.
|
| |
J Biol Chem,
280,
32775-32783.
|
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|
|
|
|
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A.Bochkarev,
and
E.Bochkareva
(2004).
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J.E.Nuss,
and
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(2004).
Denaturation of replication protein A reveals an alternative conformation with intact domain structure and oligonucleotide binding activity.
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Protein Sci,
13,
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Coordinated regulation of replication protein A activities by its subunits p14 and p32.
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J Biol Chem,
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M.E.Stauffer,
and
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Physical interaction between replication protein A and Rad51 promotes exchange on single-stranded DNA.
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J Biol Chem,
279,
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M.F.Fernández,
R.R.Castellari,
F.F.Conte,
F.C.Gozzo,
A.A.Sabino,
H.Pinheiro,
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Identification of three proteins that associate in vitro with the Leishmania (Leishmania) amazonensis G-rich telomeric strand.
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Eur J Biochem,
271,
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M.P.Egloff,
F.Ferron,
V.Campanacci,
S.Longhi,
C.Rancurel,
H.Dutartre,
E.J.Snijder,
A.E.Gorbalenya,
C.Cambillau,
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The severe acute respiratory syndrome-coronavirus replicative protein nsp9 is a single-stranded RNA-binding subunit unique in the RNA virus world.
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Proc Natl Acad Sci U S A,
101,
3792-3796.
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PDB code:
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P.E.Pestryakov,
D.Y.Khlimankov,
E.Bochkareva,
A.Bochkarev,
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Human replication protein A (RPA) binds a primer-template junction in the absence of its major ssDNA-binding domains.
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Nucleic Acids Res,
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Recruitment of replication protein A by the papillomavirus E1 protein and modulation by single-stranded DNA.
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J Virol,
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A.I.Arunkumar,
M.E.Stauffer,
E.Bochkareva,
A.Bochkarev,
and
W.J.Chazin
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Independent and coordinated functions of replication protein A tandem high affinity single-stranded DNA binding domains.
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J Biol Chem,
278,
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C.R.Cook,
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F.C.Peterson,
B.F.Volkman,
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A novel zinc finger is required for Mcm10 homocomplex assembly.
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J Biol Chem,
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Nucleic acid recognition by OB-fold proteins.
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K.M.Larsson,
S.Bodevin,
M.Atta,
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B.M.Sjoberg,
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(2003).
A metal-binding site in the catalytic subunit of anaerobic ribonucleotide reductase.
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Proc Natl Acad Sci U S A,
100,
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PDB code:
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I.D.Kerr,
R.I.Wadsworth,
L.Cubeddu,
W.Blankenfeldt,
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Insights into ssDNA recognition by the OB fold from a structural and thermodynamic study of Sulfolobus SSB protein.
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| |
EMBO J,
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PDB code:
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I.M.Wyka,
K.Dhar,
S.K.Binz,
and
M.S.Wold
(2003).
Replication protein A interactions with DNA: differential binding of the core domains and analysis of the DNA interaction surface.
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Biochemistry,
42,
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M.Lei,
E.R.Podell,
P.Baumann,
and
T.R.Cech
(2003).
DNA self-recognition in the structure of Pot1 bound to telomeric single-stranded DNA.
|
| |
Nature,
426,
198-203.
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|
PDB codes:
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|
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|
|
|
|
|
P.E.Pestryakov,
K.Weisshart,
B.Schlott,
S.N.Khodyreva,
E.Kremmer,
F.Grosse,
O.I.Lavrik,
and
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(2003).
Human replication protein A. The C-terminal RPA70 and the central RPA32 domains are involved in the interactions with the 3'-end of a primer-template DNA.
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J Biol Chem,
278,
17515-17524.
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S.Hattingh-Willis,
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L.B.Rothman-Denes
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Phage N4 RNA polymerase II recruitment to DNA by a single-stranded DNA-binding protein.
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Genes Dev,
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S.K.Binz,
Y.Lao,
D.F.Lowry,
and
M.S.Wold
(2003).
The phosphorylation domain of the 32-kDa subunit of replication protein A (RPA) modulates RPA-DNA interactions. Evidence for an intersubunit interaction.
|
| |
J Biol Chem,
278,
35584-35591.
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S.S.Krishna,
I.Majumdar,
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N.V.Grishin
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Structural classification of zinc fingers: survey and summary.
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31,
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P.D.Jeffrey,
J.Miller,
E.Kinnucan,
Y.Sun,
N.H.Thoma,
N.Zheng,
P.L.Chen,
W.H.Lee,
and
N.P.Pavletich
(2002).
BRCA2 function in DNA binding and recombination from a BRCA2-DSS1-ssDNA structure.
|
| |
Science,
297,
1837-1848.
|
|
|
PDB codes:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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